Category Archives: General Microbiome

January 14, 2018

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Today’s digest features brilliant ‘Letters to the Editors’ articles in response to recently published works, and concise microbiome reviews. Lastly, an improved method for assembly of functional metagenomes.

Gut Microbiome

Letters to the Editor: Navigating the Microbiota Seas: Triangulation Finds a Way Forward. Rosen, CE. Cell Host & Microbe.

Perturbations of the gut microbiome genes in infants with atopic dermatitis according to feeding type. Lee, M-J. Journal of Allergy and Clinical Immunology

Insect Microbiome

REVIEW: Functional roles and metabolic niches in the honey bee gut microbiota. Bonilla-Rosso, G. Current Opinion in Microbiology

Letters to the Editor: Insect Gut Microbiota: Accessories to the Bite. Aksoy, S. Cell Host & Microbe

Animal Experiments and Microbiome

Characterisation of the intestinal microbial communities of rainbow trout (Oncorhynchus mykiss) fed with Hermetia illucens (black soldier fly) partially defatted larva meal as partial dietary protein source. Bruni, L. Aquaculture

REVIEW: Gastrointestinal tract (gut) health in the young pig. Pluske, JR. Animal Nutrition

Plant, soil, and water Microbiome

Deciphering the bacterial and fungal communities in clubroot-affected cabbage rhizosphere treated with Bacillus Subtilis XF-1. Liu, C. Agriculture, Ecosystems & Environment

REVIEW:Rhizospheric microorganisms as a solution for the recovery of soils contaminated by petroleum: A review. Janzen dos Santos, J. Journal of Environmental Management.

Food Microbiome

Different temperatures select distinctive acetic acid bacteria species and promotes organic acids production during Kombucha tea fermentation. De Filippis. Food Microbiology

Techniques/Protocol

REVIEW: Fluorescence activated cell-sorting principles and applications in microalgal biotechnology. Pereira, H. Algal Research

A-GAME: improving the assembly of pooled functional metagenomics sequence data. Chiara, M. BMC Genomics

Microbes in the News

Research Says Exercise Also Improves Your Gut Bacteria

-Healthline

January 13, 2018

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100+ alerts, meaning great papers in every category. Enjoy!

General microbiome
Review: Sphingolipids in host-microbial interactions – Stacey L Heaver – Current Opinion In Microbiology

Editorial: The Human Microbiome – Emily P Balskus – ACS Infectious Diseases

Review: Emergent Heterogeneous Micro-environments in Biofilms:Substratum Surface Heterogeneity and Bacterial Adhesion Force-sensing – Yijin Ren – Fems Microbiology Reviews

Pregnancy and early life
Maturation of the gut microbiome and risk of asthma in childhood – Jakob Stokholm – Nature Communications

Haemophilus is overrepresented in the nasopharynx of infants hospitalized with RSV infection and associated with increased viral load and enhanced mucosal CXCL8 responses – Thomas H A Ederveen – Microbiome

Fetal and early life antibiotics exposure and very early onset inflammatory bowel disease: a population-based study – Anne K Örtqvist – Gut

Review: Early Microbes Modify Immune System Development and Metabolic Homeostasis-The “Restaurant” Hypothesis Revisited – Michael J Nash – Frontiers In Endocrinology

Human respiratory microbiome
Genomics of Corynebacterium striatum, an emerging multi-drug resistant pathogen of immunocompromised patients – Kathleen Nudel – Clinical Microbiology And Infection

Human skin microbiome
Transcriptomic profiling of interacting nasal staphylococci species reveals global changes in gene and non-coding RNA expression – Grith M M Hermansen – Fems Microbiology Letters

Human oral microbiome
Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer – Richard B Hayes – JAMA Oncology

Composition of salivary microbiota in elderly subjects – Taiji Ogawa – Scientific Reports

Human gut microbiome
CX3CR1+ mononuclear phagocytes control immunity to intestinal fungi – Irina Leonardi – Science (New York, N.Y.)

Antagonism toward the intestinal microbiota and its effect on Vibrio cholerae virulence. – Wenjing Zhao – Science (New York, N.Y.)

Evaluation of bloodstream infections, Clostridium difficile infections, and gut microbiota in pediatric oncology patients – Bryan T. Nycz – PLoS One

Antibiotic Treatments for Clostridium difficile Infection Are Associated with Distinct Bacterial and Fungal Community Structures – Regina Lamendella – mSphere

Alterations of the gut microbiota in Hashimoto’s thyroiditis patients – Fuya Zhao – Thyroid : Official Journal Of The American Thyroid Association

Structural insights into a family 39 glycoside hydrolase from the gut symbiont Bacteroides cellulosilyticus WH2 – Ahmad Ali-Ahmad – Journal Of Structural Biology

Review: Gut Microbiota Dysbiosis Drives and Implies Novel Therapeutic Strategies for Diabetes Mellitus and Related Metabolic Diseases – Xuan Li – Frontiers In Immunology

Review: Pathogens, microbiome and the host: emergence of the ecological Koch’s postulates – Pascale Vonaesch – FEMS Microbiology Reviews

Review: Biochemistry of Complex Glycan Depolymerisation by the Human Gut Microbiota – Didier Ndeh – FEMS Microbiology Reviews

Review: Segmented filamentous bacteria, Th17 inducers and helpers in a hostile world – Pamela Schnupf – Current Opinion In Microbiology

Microbial Ecology
Simulation of Escherichia coli Dynamics in Biofilms and Submerged Colonies with an Individual-Based Model Including Metabolic Network Information – Ignace L M M Tack – Frontiers In Microbiology

Initial evenness determines diversity and cell density dynamics in synthetic microbial ecosystems – Elham Ehsani – Scientific Reports

Pan-genome analysis of the genus Finegoldia identifies two distinct clades, strain-specific heterogeneity, and putative virulence factors – Holger Brüggemann – Scientific Reports

Specifying the Harsh Conditions of Life: Resource Competition and Predation in the 1970s – Alita R. Burmeister – The American Naturalist

Animal experiments
Maternal metabolic, immune, and microbial systems in late pregnancy vary with malnutrition in mice – Kristin L Connor – Biology of Reproduction

Fecal Microbiota Transplantation, Commensal Escherichia coli and Lactobacillus johnsonii Strains Differentially Restore Intestinal and Systemic Adaptive Immune Cell Populations Following Broad-spectrum Antibiotic Treatment – Ira Ekmekciu – Frontiers In Microbiology

Impacts of feeding preweaned calves milk containing drug residues on the functional profile of the fecal microbiota – Richard Van Vleck Pereira – Scientific Reports

Gama-aminobutyric Acid Enriched Rice Bran Diet Attenuates Insulin Resistance and Balances Energy Expenditure via Modification of Gut Microbiota and SCFAs – Xu Si – Journal Of Agricultural And Food Chemistry

Proton Pump Inhibitors Increase the Susceptibility of Mice to Oral Infection with Enteropathogenic Bacteria – Eiichiro Yasutomi – Digestive Diseases And Sciences

Rhubarb supplementation promotes intestinal mucosal innate immune homeostasis through modulating intestinal epithelial microbiota in goat kids – Jinzhen Jiao – Journal Of Agricultural And Food Chemistry

Impact of dietary induced precocious gut maturation on cecal microbiota and its relation to the blood-brain barrier during the postnatal period in rats – N Marungruang – Neurogastroenterology And Motility : The Official Journal Of The European Gastrointestinal Motility Society

Exercise Prevents Enhanced Postoperative Neuroinflammation and Cognitive Decline and Rectifies the Gut Microbiome in a Rat Model of Metabolic Syndrome – Xiaomei Feng – Frontiers In Immunology

Rifampicin treatment of Blattella germanica evidences a fecal transmission route of their gut microbiota – Tania Rosas – Fems Microbiology Ecology

Gut Flora-Dependent Metabolite Trimethylamine-N-oxide Accelerates Endothelial Cell Senescence and Vascular Aging through Oxidative Stress – Yilang Ke – Free Radical Biology & Medicine

Nanocomposite of Half-Fin Anchovy Hydrolysates/Zinc Oxide Nanoparticles Exhibits Actual Non-Toxicity and Regulates Intestinal Microbiota, Short-Chain Fatty Acids Production and Oxidative Status in Mice – Ru Song – Marine Drugs

Animal microbiome
Is there a link between aging and microbiome diversity in exceptional mammalian longevity? – Graham M. Hughes – PeerJ (Specifically, bats or Myotis myotis)

Gut Microbes Egested during Bites of Infected Sand Flies Augment Severity of Leishmaniasis via Inflammasome-Derived IL-1β – Ranadhir Dey – Cell Host & Microbe

The Sarda Sheep Host Fecal Proteome – Antonio Palomba – Proteomics

Host Specificity for Bacterial, Archaeal and Fungal Communities Determined for High- and Low-Microbial Abundance Sponge Species in Two Genera – Maryam Chaib De Mares – Frontiers In Microbiology (from December 2017)

Comparative Metagenomics of Cellulose- and Poplar Hydrolysate-Degrading Microcosms from Gut Microflora of the Canadian Beaver (Castor canadensis) and North American Moose (Alces americanus) after Long-Term Enrichment. – Mabel T Wong – Frontiers In Microbiology (from December 2017)

Regular Wounding in a Natural System: Bacteria Associated With Reproductive Organs of Bedbugs and Their Quorum Sensing Abilities – Oliver Otti – Frontiers In Immunology

Plant, root, and soil microbiome
Forest conversion induces seasonal variation in microbial β-diversity – Shengen Liu – Environmental Microbiology

Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere – Hector Urbina – Fungal Biology

Different impacts of manure and chemical fertilizers on bacterial community structure and antibiotic resistance genes in arable soils – Peng Liu – Chemosphere

Intra-species variation in a widely distributed tree species regulates the responses of soil microbiome to different temperature regimes – Cui-Jing Zhang – Environmental Microbiology Reports

Positive diversity-functioning relationships in model communities of methanotrophic bacteria – Elvira Schnyder – Ecology

Plant Phylogeny and Life History Shape Rhizosphere Bacterial Microbiome of Summer Annuals in an Agricultural Field – Bryan D. Emmett – Frontiers in Microbiology (from December 2017)

Soil microbial communities and enzyme activities in sea-buckthorn (Hippophae rhamnoides) plantation at different ages – Miao Yang – Plos One

The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics – Mohammad Bahram – Environmental Microbiology Reports

Ecological mechanisms underlying soil bacterial responses to rainfall along a steep natural precipitation gradient – Bonnie Waring – FEMS Microbiology Ecology

Review: Current Insights into the Role of Rhizosphere Bacteria in Disease Suppressive Soils – Ruth Gómez Expósito – Frontiers in Microbiology (from December 2017)

Water and extremophile microbiome
Microbially mediated aluminosilicate formation in acidic anaerobic environments: A cell-scale chemical perspective – J. Sánchez-España – GeoBiology

Responses of Periphyton to Fe2O3 Nanoparticles: A Physiological and Ecological Basis for Defending Nanotoxicity – Jun Tang – Environmental Science & Technology

Variations in bacterial and archaeal communities along depth profiles of Alaskan soil cores – Binu Mani Tripathi – Scientific Reports

Microbiological and Geochemical Survey of CO2-Dominated Mofette and Mineral Waters of the Cheb Basin, Czech Republic – Patryk Krauze – Frontiers In Microbiology

In Situ Field Sequencing and Life Detection in Remote (79°26’N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities – J Goordial – Frontiers In Microbiology (from December 2017)

Built environment
Diversity of Microbial Communities and Quantitative Chemodiversity in Layers of Marine Sediment Cores from a Causeway (Kaichu-Doro) in Okinawa Island, Japan – Taha Soliman – Frontiers In Microbiology

Microbial Contamination on Touch Surfaces in Sick- and Well-Child Waiting Rooms in Pediatric Outpatient Facilities – Irina Gudakova – The Pediatric Infectious Disease Journal

Biostimulation and bioaugmentation of native microbial community accelerated bioremediation of oil refinery sludge – Ajoy Roy – Bioresource Technology

Temporal variation in bacterial and methanogenic communities of three full-scale anaerobic digesters treating swine wastewater – Gyuseong Han – Environmental Science And Pollution Research International

Microbial community of a gasworks aquifer and identification of nitrate-reducing Azoarcus and Georgfuchsia as key players in BTEX degradation – Martin Sperfeld – Water Research

Review: Microbiome analysis and -omics studies of microbial denitrification processes in wastewater treatment: recent advances – Lili Miao – Science China. Life Sciences

Food microbiology
Absorption and Metabolism of Phenolics from Digests of Polyphenol-Rich Potato Extracts Using the Caco-2/HepG2 Co-Culture System – Shima Sadeghi Ekbatan – Foods (Basel, Switzerland)

Effects of polysaccharides from purple sweet potatoes on immune response and gut microbiota composition in normal and cyclophosphamide treated mice – Chao Tang – Food & Function

A Combined LC-MS Metabolomics- and 16S rRNA Sequencing Platform to Assess Interactions between Herbal Medicinal Products and Human Gut Bacteria in Vitro: a Pilot Study on Willow Bark Extract – Eva-Maria Pferschy-Wenzig – Frontiers In Pharmacology

Review: Inflammatory Bowel Diseases and Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols: An Overview – Sandra Maria Barbalho – Journal Of Medicinal Food

Probiotics / prebiotics / antibiotics
The antimicrobial peptide SAAP-148 combats drug-resistant bacteria and biofilms – Anna de Breij – Science Translational Medicine

Low amounts of dietary fibre increase in vitro production of short-chain fatty acids without changing human colonic microbiota structure – Daisuke Sasaki – Scientific Reports

Single Cell Observations Show Persister Cells Wake Based on Ribosome Content – Jun-Seob Kim – bioRxiv

Evidence for PMAT- and OCT-like biogenic amine transporters in a probiotic strain of Lactobacillus: Implications for interkingdom communication within the microbiota-gut-brain axis. – Mark Lyte – Plos One

Phages and viruses
Metagenomic Virome Analysis of Culex Mosquitoes from Kenya and China. – Evans Atoni – Viruses

Virus Dynamics Are Influenced by Season, Tides and Advective Transport in Intertidal, Permeable Sediments – Verona Vandieken – Frontiers In Microbiology

Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis – Soner Yildiz – Microbiome

Genome Announcements
Draft Genome Sequence of Megamonas funiformis Strain Marseille-P3344, Isolated from a Human Fecal Microbiota. – Mossaab Maaloum – Genome Announcements

Draft Genome Sequences of Bifidobacterium Strains N4G05 and N5G01, Isolated from the Human Vaginal Microbiome. – Aline C Freitas – Genome Announcements

‘Lactomassilus timonensis,’ a new anaerobic bacterial species isolated from the milk of a healthy African mother – A H Togo – New Microbes And New Infections

Microbes in the news
AGA enrolls 1st patient into largest planned fecal microbiota transplantation study – Eric Oliver – GI & Endoscopy

Will This Swallowable Sensor Replace Colonoscopies? – Bob Curley – HealthLine

**A Patient’s Journey: Taming the Glucose Monster – Howard Wolinsky – MedPage Today**

Microbes on the market
CoreBiome Bolsters Its Board of Directors with the Addition of Daniel Pomp, Ph.D. – BusinessWire

Curetis and MGI Advance Strategic Partnership in NGS-Based Molecular Microbiology – BioSpace

Science, publishing, and career
“Available upon request”: not good enough for microbiome data! – Morgan G I Langille – Microbiome

Tiffany’s non-microbiology picks
Chemists go green to make better blue jeans – Nature
I did not know demin was so dirty until I heard about Everlane’ new jeans – and now there are new method to make them!

January 11, 2018

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Today’s Microbiome Digest is quite long, since it contains alerts from two days. There are many interesting articles in Gut, Plant and Water Microbiome Sections. Interesting review to highlight is from L. Tipton about lung mycobiome  and the one from D. Rose Ewald about human microbiota. Today we also have quite few articles about viruses, among which P.C. Hsu revails gene targets of Ebola virus microRNAs involved in the human skin microbiome,  S. S. Jagdale reports on  mutualistic interactions of viruses with lower eukaryotes and C. Winter explains how mixing alters the lytic activity of viruses in the dark ocean.

General microbiome

Complete genomic characterisation of two Escherichia coli lineages responsible for a cluster of carbapenem resistant infections in a Chinese hospital – Zhiyong Zong – bioRxiv

Geometrical Distribution of Cryptococcus neoformans Mediates Flower-Like Biofilm Development – William Lopes – Frontiers in Microbiology

Pregnancy and early life

Editorial: The Neonatal Immune System: A Unique Host-Microbial Interface – Joseph M. Bliss – Frontiers in Pediatrics

Modeling Metabolic Interactions in a Consortium of the Infant Gut Microbiome – Francisco Pinto – Frontiers in Microbiology

Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains – Silvia Arboleya – Genomics

Early-life gut microbiome and egg allergy – Mina Fazlollahi – Allergy

Human respiratory microbiome

Perspective: Fungal Microbiota in Chronic Airway Inflammatory Disease and Emerging Relationships with the Host Immune Response – Irene Zhang – Frontiers in Microbiology

Microbiome and asthma – Milena Sokolowska – Asthma Research and Practice

Review: The lung mycobiome in the next-generation sequencing era – Laura Tipton – Virulence

The lung tissue microbiota of mild and moderate chronic obstructive pulmonary disease – Alexa A. Pragman – Microbiome

 Oral microbiome

Profiling of subgingival plaque biofilm microbiota in female adult patients with clear aligners: a three-month prospective study – Runzhi Guo – PeerJ

Ecological Approaches to Dental Caries Prevention: Paradigm Shift or Shibboleth? – Nebu Philip  – Caries Research

Human skin microbiome

On revealing the gene targets of Ebola virus microRNAs involved in the human skin microbiome – Pei-Chun Hsu – PeerJ

Temporal Variation of the Skin Bacterial Community and Batrachochytrium dendrobatidis Infection in the Terrestrial Cryptic Frog Philoria loveridgei – Mariel Familiar López – Frontiers in Microbiology

Human vaginal microbiome

Microbiota-based analysis reveals specific bacterial traits and a novel strategy for the diagnosis of infectious infertility – Simon Graspeuntner – PLOS One

Human nearly-sterile sites 

Culture-independent analysis of liver abscess using nanopore sequencing – Liang Gong – PLOS One

Human gut microbiome

The Gut Microbiome and Control of Weight Gain – Anita L. Kozyrskyj – Pediatric Obesity

Immunosuppressive effect of the gut microbiome altered by high-dose tacrolimus in mice – Z. Zhang – American Journal of Transplatation

Review: Human microbiota, blood group antigens, and disease – D. Rose Ewald – WIREs

Microbiome, Immunomodulation, and the Neuronal System – Eric Marietta – Neurotherapeutics

Editorial: Improve gut microbiome: a new horizon of cancer therapy – Hiroshi Fukui – Hepatobiliary Surgery and Nutrition

The Gut Microbiome and Multiple Sclerosis – Javier Ochoa-Repáraz – Cold Spring Harbor Perspectives in Medicine

Genomic diversity and distribution of Bifidobacterium longum subsp. longum across the human lifespan – Toshitaka Odamaki – Scientific Reports

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome – Melanie Schirmer – Nature Microbiology

Links between Dietary Protein Sources, the Gut Microbiota, and Obesity – Lise Madsen – Frontiers in Physiology

Ceftriaxone promotes the emergence of AmpC-overproducing Enterobacteriaceae in gut microbiota from hospitalized patients – Victoire de Lastours – European Journal of Clinical Microbiology & Infectious Diseases

Functional analysis of arginine decarboxylase gene speA of Bacteroides dorei by markerless gene deletion – Mikiyasu Sakanaka – FEMS Microbiology Letters

SadA-Expressing Staphylococci in the Human Gut Show Increased Cell Adherence and Internalization – Arif Luqman – Cell Reports

Gut microbiome populations are associated with structure-specific changes in white matter architecture – Irene M. Ong – Translational Psychiatry

Spatiotemporally Heterogeneous Population Dynamics of Gut Bacteria Inferred from Fecal Time Series Data – Hidetoshi Inaminea – mBio

Animal experiments 

Identification of a protective B-cell epitope of the Staphylococcus aureus GapC protein by screening a phage-displayed random peptide library – Mengyao Wang – PLOS One

Lactobacillus plantarum CCFM10 alleviating oxidative stress and restoring the gut microbiota in D-galactose-induced aging mice – Jichun Zhao – Food and Function

Effect of dark sweet cherry powder consumption on the gut microbiota, short-chain fatty acids, and biomarkers of gut health in obese db/db mice – Jose F. Garcia-Mazcorro – PeerJ

Dietary Corn Bran Fermented by Bacillus subtilis MA139 Decreased Gut Cellulolytic Bacteria and Microbiota Diversity in Finishing Pigs – Ping Liu – Frontiers in Cellular and Infection Microbiology

Intestinal and Systemic Immune Responses upon Multi-drug Resistant Pseudomonas aeruginosa Colonization of Mice Harboring a Human Gut Microbiota – Eliane von Klitzing – Frontiers in Microbiology

Modulation of Intestinal Microbiome Prevents Intestinal Ischemic Injury – Alessandra Bertacco – Frontiers in Physiology

Animal microbiome 

Influence of fruit and invertebrate consumption on the gut microbiota of wild white-faced capuchins (Cebus capucinus) – Elizabeth K. Mallott – American Journal of Physical Anthropology

Differential Ecological Specificity of Protist and Bacterial Microbiomes across a Set of Termite Species – Lena Waidele – Frontiers in Microbiology

Molecular identification and phylogenetic analysis of Bothrops insularis bacterial and fungal microbiota – Lidiane Nunes Barbosa – Journal of Toxicology and Environmental Health

Plant, root, and soil microbiome

Diazotroph abundance and community composition in an acidic soil in response to aluminum-tolerant and aluminum-sensitive maize (Zea mays L.) cultivars under two nitrogen fertilizer forms – Chao Wang – Plant and Soil

The influence of microbial communities for triadimefon enantiomerization in soils with different pH values – Khaled Mohamed Ahmed Talab – Chirality

Antimony Redox Biotransformation in the Subsurface: Effect of Indigenous Sb(V) Respiring Microbiota – Liying Wang – Encironmental Science and Technology

Biostimulant Action of Protein Hydrolysates: Unraveling Their Effects on Plant Physiology and Microbiome – Giuseppe Colla – Frontiers in Plant Science

Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria – Hongwei Liu – Frontiers in Microbiology

Bacillus amyloliquefaciens L-S60 Reforms the Rhizosphere Bacterial Community and Improves Growth Conditions in Cucumber Plug Seedling – Yuxuan Qin – Frontiers in Microbiology

Exploring the Microbiota of Faba Bean: Functional Characterization of Lactic Acid Bacteria – Michela Verni –  Frontiers in Microbiology

Contribution of Zinc Solubilizing Bacteria in Growth Promotion and Zinc Content of Wheat – Sana Kamran – Frontiers in Microbiology

Application of Endophytic Pseudomonas fluorescens and a Bacterial Consortium to Brassica napus Can Increase Plant Height and Biomass under Greenhouse and Field Conditions –  Richard D. Lally – Frontiers in Microbiology

Exploiting rhizosphere microbial cooperation for developing sustainable agriculture strategies – Yoann Besset-Manzoni – Environmental Science and Pollution Research

Dynamics of oxygen and carbon dioxide in rhizospheres of Lobelia dortmanna – a planar optode study of belowground gas exchange between plants and sediment – Nikola Lenzewski – New Phytologist

Characterization of Microbial Communities in Acidified, Sulfur Containing Soils – Grzegorz Czerwonka – Polish Journal of Microbiology

Comparison of Microbial Communities Associated with Halophyte (Salsola stocksii) and Non-Halophyte (Triticum aestivum) Using Culture-Independent Approaches – Salma Mukhtar – Polish Journal of Microbiology

Water and extremophile microbiome 

Data-mining of Antibiotic Resistance Genes Provides Insight into the Community Structure of Ocean Microbiome – Shiguang Hao – bioRxiv

Mixing alters the lytic activity of viruses in the dark ocean – Christian Winter – Ecology

Biological Characterization of Microenvironments in a Hypersaline Cold Spring Mars Analog – Haley M. Sapers – Frontiers in Microbiology

Patterns and Drivers of Vertical Distribution of the Ciliate Community from the Surface to the Abyssopelagic Zone in the Western Pacific Ocean – Feng Zhao – Frontiers in Microbiology

Aerobic and Anaerobic Methanotrophic Communities Associated with Methane Hydrates Exposed on the Seafloor: A High-Pressure Sampling and Stable Isotope-Incubation Experiment – David H. Case – Frontiers in Microbiology

A Multi-season Investigation of Microbial Extracellular Enzyme Activities in Two Temperate Coastal North Carolina Rivers: Evidence of Spatial but Not Seasonal Patterns – Avery Bullock – Frontiers in Microbiology

Functional Stability and Community Dynamics during Spring and Autumn Seasons Over 3 Years in Camargue Microbial Mats – Mercedes Berlanga – Frontiers in Microbiology

Oxygenation of Hypoxic Coastal Baltic Sea Sediments Impacts on Chemistry, Microbial Community Composition, and Metabolism – Elias Broman – Frontiers in Microbiology

Exploring the Cultivable Ectocarpus Microbiome – Hetty KleinJan – Frontiers in Microbiology

Phylogenetic Structure and Metabolic Properties of Microbial Communities in Arsenic-Rich Waters of Geothermal Origin – Simona Crognale – Frontiers in Microbiology

Prokaryotic Community Composition in Arctic Kongsfjorden and Sub-Arctic Northern Bering Sea Sediments As Revealed by 454 Pyrosequencing – Yin-Xin Zeng – Frontiers in Microbiology

Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium – Elham Karimi – Frontiers in Microbiology

Comparative genomics highlights symbiotic capacities and high metabolic flexibility of the marine genus Pseudovibrio  – Dennis Versluis – GBE Genome BIology and Evolution

Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases – Andrea G. Bravo – ISME

Dynamics of phytoplankton and heterotrophic bacterioplankton in the western tropical South Pacific Ocean along a gradient of diversity and activity of diazotrophs – France Van Wambeke – Biogeosciences

Microbial methanogenesis in the sulfate-reducing zone of sediments in the Eckernförde Bay, SW Baltic Sea – Johanna Maltby – Biogeosciences

Built environment

Control of corrosive bacterial community by bronopol in industrial water system – Jayaraman Narenkumar – 3 Biotech

A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities –  Manuel Kleiner – bioRxiv

Uncovering the Potential of Termite Gut Microbiome for Lignocellulose Bioconversion in Anaerobic Batch Bioreactors – Lucas Auer – Frontiers in Microbiology

Microbial Communities Shaped by Treatment Processes in a Drinking Water Treatment Plant and Their Contribution and Threat to Drinking Water Safety – Qi Li – Frontiers in Microbiology

Food microbiology

Development of novel quinoa-based yoghurt fermented with dextran producer Weissella cibaria MG1 – Emanuele Zannini – International Journal of Food Microbiology

Bacterial Community and Spoilage Profiles Shift in Response to Packaging in Yellow-Feather Broiler, a Highly Popular Meat in Asia – Huhu Wang – Frontiers in Microbiology

Metagenomic Profiling of the Bacterial Community Changes from Koji to Mash Stage in the Brewing of Soy Sauce – Hongbin Wang – Polish Journal of Microbiology

Probiotics / prebiotics

Probiotics or Pro-healers the Role of Beneficial Bacteria in Tissue Repair – Jovanka Lukic – Wound Reparation and Regeneration

Probiotic Lactobacillus sp. inhibit growth, biofilm formation and gene expression of caries-inducing Streptococcus mutans – Reham Wasfi – Journal of Cellular and Molecular Medicine

A mixture of Lactobacillus species isolated from traditional fermented foods promote recovery from antibiotic-induced intestinal disruption in mice – Ying Shi – Journal of Applied Microbiology

Beneficial changes in rumen bacterial community profile in sheep and dairy calves as a result of feeding the probiotic Bacillus amyloliquefaciens H57 – Benjamin J Schofield – Journal of Applied Microbiology

Phages and viruses

Enemies with benefits: mutualistic interactions of viruses with lower eukaryotes – Shounak S. Jagdale – Archives of Virology

Biogeography & environmental conditions shape bacteriophage-bacteria networks across the human microbiome – Geoffrey D. Hannigan – bioRxiv

Investigation of prevalence of free Shiga toxin-producing Escherichia coli (STEC)-specific bacteriophages and its correlation with STEC bacterial hosts in a produce-growing area in Salinas, California – Yen-Te Liao – PLOS One

Component tree analysis of cystovirus φ6 nucleocapsid Cryo-EM single particle reconstructions – Lucas M. Oliveira – PLOS One

Bioinformatics

HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments – Nicholas D. Youngblut – PLOS One

Biotechnology

Cyanobacterial diversity held in microbial biological resource centers as a biotechnological asset: the case study of the newly established LEGE culture collection – Vitor Ramos – Journal of Applied Phycology

Rapidly moving new bacteria to model-organism status – Hualan Liu – Current Opinion in Biotechnology

Techniques

Development of a biosensor protein bullet as a fluorescent method for fast detection of Escherichia coli in drinking water – Ignacio Gutiérrez-del-Río – PLOS One

Research Note: Methods for detecting Gemmata spp. bacteremia in the microbiology laboratory – Jacques-Robert Christen – BMS Genomics

A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities – Manuel Kleiner – bioRxiv

Microbes in the news 

Gene/cell connection provides new insight into how our gut microbiome stays healthy

A powerful new weapon against drug-resistant bacteria was inspired by the human body

ASU developing biodegradable plastics made from bacteria

Pharmaceutical Pollution Drives Microbial Resistance in Urban Streams

Microbes and Art

This scientist creates ephemeral works of art with bioluminescent bacteria

January 8, 2018

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Today’s Microbiome Digest has many interesting articles. Read how microscope-based artificial intelligence could alleviate shortage of clinical microbiologists, the article by K. P. Smith. N. A. Kamennaya reports on “Pomacytosis”, a semi-extracellular phagocytosis of cyanobacteria, while M. F. Dias investigated the effect of different drinking waters on mouse gut microbiota.

Events

One-day Symposium (12 Jan 2018): Microbial symbiosis in the marine environment – live streamming

Jobs

Postdoctoral positions in evolutionary genomics, UT Austin

General microbiome

Dietary trehalose enhances virulence of epidemic Clostridium difficile – J. Collins – Nature

Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla – Frederick M. Cohan – Microbiology Spectrum

How much do rRNA gene surveys underestimate extant bacterial diversity? – Luis M. Rodriguez-R – Applied and Environmental Microbiology

Vibrio cholerae genomic diversity within and between patients –  Inès Levade – Microbial Genomics

Automated Interpretation of Blood Culture Gram Stains using a Deep Convolutional Neural Network – Kenneth P. Smith – Applied and Environmental Microbiology

Regulated ploidy of Bacillus subtilis and three new isolates of Bacillus and Paenibacillus – Benjamin Böttinger – FEMS Microbiology Letters

Human respiratory microbiome

Heavy metal exposure and nasal Staphylococcus aureus colonization: analysis of the National Health and Nutrition Examination Survey (NHANES) – Shoshannah Eggers – Environmental Health

Oral microbiome

Microbial Analysis of Endodontic Infections in Root-filled Teeth with Apical Periodontitis before and after Irrigation Using Pyrosequencing – Homan Zandi – Journal of Endodontics

Human vaginal microbiome

Long-term Lactobacillus rhamnosus BMX 54 application to restore a balanced vaginal ecosystem: a promising solution against HPV-infection – Ettore Palma – BMC Infectious Diseases

Lactobacillus-deficient vaginal microbiota dominate post-partum women in rural Malawi – Ronan Doyle – Applied and Environmental Microbiology

Human nearly-sterile sites

Microbiota and the liver – Ting-Chin David Shen – Liver Transplatation

Human gut microbiome

Comparison of DNA extraction methods for human gut microbial community profiling – Mi Young Lim – Systematic and Applied Microbiology

Changes in Gut Microbiota–Related Metabolites and Long-term Successful Weight Loss in Response to Weight-Loss Diets: The POUNDS Lost Trial – Yoriko Heianza – Diabetes Care

Adaptation of human gut microbiota to bariatric surgeries in morbidly obese patients: A systematic review – Hanieh-Sadat Ejtahed – Microbial Pathogenesis

The germ-organ theory of non-communicable diseases – Mariana X. Byndloss – Nature Reviews Microbiology

Evolution of a dominant natural isolate of Escherichia coli in the human gut over a year suggests a neutral evolution with reduced effective population size – Mohamed Ghalayini – Applied and Environmental Microbiology

Animal experiments

Changes in mouse gut bacterial community in response to different types of drinking water – Marcela F. Dias – Water Research

Plant, root, and soil microbiome

Microbial Communities of High-Elevation Fumaroles, Penitentes, and Dry Tephra “Soils” of the Puna de Atacama Volcanic Zone – Adam J. Solon – Microbial Ecology

Shifts in soil bacterial and archaeal communities during freeze-thaw cycles in a seasonal frozen marsh, Northeast China – Jiusheng Ren – Science of The Total Environment

The ‘Neglected’ Soil Virome – Potential Role and Impact – Akbar Adjie Pratama – Trends in Microbiology

Water and extremophile microbiome 

Study of marine bacteria inactivation by photochemical processes: disinfection kinetics and growth modeling after treatment – Javier Moreno-Andrés – Environmental Science and Pollution Research

Metabolic capability and in situ activity of microorganisms in an oil reservoir – Yi-Fan Liu – Microbiome

Phylogenetic distribution of roseobacticides in the Roseobacter group and their effect on microalgae – Eva C Sonnenschein – BioRxiv

“Pomacytosis”—Semi-extracellular phagocytosis of cyanobacteria by the smallest marine algae – Nina A. Kamennaya – PLOS Biology

The Green Berry Consortia of the Sippewissett Salt Marsh: Millimeter-Sized Aggregates of Diazotrophic Unicellular Cyanobacteria – Elizabeth G. Wilbanks – Frontiers in Microbiology

Dynamic changes in carbonate chemistry in the microenvironment around single marine phytoplankton cells – Abdul Chrachri – Nature Communications

Homogenization of lake cyanobacterial communities over a century of climate change and eutrophication – Marie-Eve Monchamp – Nature Ecology & Evolution

Bacterial Recycling of Archaeal Biomass as a New Strategy for Extreme Life in the Dead Sea Deep Sediment – Camille Thomas – EarthArXiv Preprints

Food microbiology

Seasonal variances in bacterial microbiota and volatile organic compounds in raw milk – Beata Nalepa – International Journal of Food Microbiology

Phages and viruses

Is weak CD4+ gain in the course of suppressive combination antiretroviral therapy for HIV infection a current clinical challenge? A case report and brief review of the literature – Camilla Tincati – BMC Infectious Diseases

Techniques

NanoAmpli-Seq: A workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform – Szymon T Calus – bioRxiv

Microbes in the news

Scientists engineer sound-reflecting bacteria

Experts: ‘Raw Water’ Offers Unfiltered Risk

 

January 5, 2018

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Today’s digest has an interesting commentary on the oral-gut connection and a brilliant piece on microbial diversity. Lastly, a look at how grapevines influence belowground diversity and networks

General Microbiome

A role for the endometrial microbiome in dysfunctional menstrual bleeding. Pelzer ES. Antonie Van Leeuwenhoek.

Performance and microbial community variations of anaerobic digesters under increasing tetracycline concentrations. Xiong Y. Applied Microbiology and Biotechnology

In Nature, There Is Only Diversity. McLaren MR. MBio.

Gut Microbiome

Commentary: Oral-gut connection: one step closer to an integrated view of the gastrointestinal tract? Lira-Junior R. Mucosal Immunology

Bile acids at the cross-roads of gut microbiome-host cardiometabolic interactions. Ryan PM. Diabeticology and Metabolic Syndrome

REVIEW: Diet, Microbiota, and Metabolic Health: Trade-Off Between Saccharolytic and Proteolytic Fermentation. Korpela K. Annual of Food Science and Technology

Nasal and Lung Microbiome

REVIEW: Fungi in Bronchiectasis: A Concise Review. Máiz L. Internatioanal Journal of Molecular Sciences

Alterations in the mucosa-associated fungal microbiota in patients with ulcerative colitis. Qiu X. Oncotarget

The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis. Luna PN. Microbiome

Fecal Microbiome

Editorial Comment: Fecal microbiota transplantation as a possible treatment of irritable bowel syndrome. Juncadella AC. Annals of Translational Medicine

Plant, Soil, and Water Microbiome

Co-variation between Distribution of Microbial Communities and Biological Metabolization of Organics in Urban Sewer Systems. Jin P. Environmental Science and Technology.

Do invasive plants structure microbial communities to accelerate decomposition in intermountain grasslands? McTee MR. Ecology and Evolution

Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality. Marasco R. Microbiome

Biodiversity of the microbial mat of the Garga hot spring. Rozanov AS. BMC Evolutionary Biology

Animal Experiments and Microbiome

Microbiota Reconstitution Does Not Cause Bone Loss in Germ-Free Mice. Quach D. mSphere

Physiological Translocation of Lactic Acid Bacteria during Pregnancy Contributes to the Composition of the Milk Microbiota in Mice. de Andrés J. Nutrients

Extreme sensitivity to ultraviolet light in the fungal pathogen causing white-nose syndrome of bats. Palmer JM. Nature Communication

OCCURRENCE OF PASTEURELLACEAE BACTERIA IN THE ORAL CAVITY OF SELECTED MARSUPIAL SPECIES. Hansen MJ. Journal of Zoo and Wildlife Medicine

Marine Microbiome

Agelas Wasting Syndrome Alters Prokaryotic Symbiont Communities of the Caribbean Brown Tube Sponge, Agelas tubulata.Deignan LK. Microbial Ecology

Environmental drivers of heterogeneity in the trophic-functional structure of protozoan communities during an annual cycle in a coastal ecosystem. Xu G. Marine Pollution Bulletin

Antibiotic Resitance

Editorial: Empiric antibiotic use in allogeneic hematopoietic cell transplantation: should we avoid anaerobe coverage? Shono Y. Blood Advances

Characterization of genetic determinants involved in antibiotic resistance in Aeromonas spp. and fecal coliforms isolated from different aquatic environments. Carnelli A. Research in Microbiology

 

 

January 2, 2018

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Happy New Year from the Microbiome Digest team!

General microbiome

Pre-print: Understanding How Microbiomes Influence The Systems They Inhabit: moving from a correlative to a causal research framework – E K Hall – bioRxiv

Human vaginal microbiome

A retrospective pilot study to determine whether the reproductive tract microbiota differs between women with a history of infertility and fertile women – Bryan A Wee – Australian and New Zealand Journal of Obstetrics and Gynaecology

Human gut microbiome

Rates of Gut Microbiome Divergence in Mammals – Alex H Nishida – Molecular Ecology

Animal microbiome

Processes shaping gut microbiota diversity in allopatric populations of the endemic lizard Podarcis lilfordi from Menorcan islets (Balearic Islands) – Laura Baldo – FEMS Microbiology Ecology

Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing – Kathrin Engel – Microbial Ecology

Plant, root, and soil microbiome

Vertical variation of a black soil’s properties in response to freeze-thaw cycles and its links to shift of microbial community structure – Ziming Han – Science of the Total Environment

Biomass, activity and structure of rhizosphere soil microbial community under different metallophytes in a mining site – Wenhao Yang – Plant and Soil

Symbiotic nitrogen fixation by rhizobia — the roots of a success story – Catherine Masson-Boivin – Current Opinion in Plant Biology

Water and extremophile microbiome

Microbial community structure and function in sediments from e-waste contaminated rivers at Guiyu area of China – Jun Liu – Environmental Pollution

Pre-print: Micro-scale ecology regulates particulate organic matter turnover in model marine microbial communities – Tim N Enke – bioRxiv

Food microbiology

Autochthonous facility-specific microbiota dominates washed-rind Austrian hard cheese surfaces and its production environment – Narciso M Quijada – International Journal of Food Microbiology

Bioinformatics

CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision – Damayanthi Herath – BMC Bioinformatics

Techniques

Serial Dilution-Based Growth Curves and Growth Curve Synchronization for High-Resolution Time Series of Bacterial Biofilm Growth – Fernando Govantes – Host-Pathogen Interactions

Microbes in the news

Fiber Is Good for You. Now Scientists May Know Why. – Carl Zimmer – The New York Times

Fast, Cheap Testing for Tuberculosis? Soon It May Be Possible – Donald G McNeil – The New York Times

How probiotics can help ward off health complications in premature babies – CTV News

Science, career, and publishing

Pre-print: Disequilibrium in Gender Ratios among Authors who Contributed Equally – Nichole A Broderick – bioRxiv

December 31, 2017

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A rich Digest to end 2017! There are several reviews on human gut microbiome and lots of papers on plant , root and soil microbiome. The airway microbiome is trending today and scientists are starting to examine rigorously the effect of herbal medicine on the gut microbiota. Happy Reading and Happy New Year!

General microbiology

Bacterial pathogens were detected from human exhaled breath using a novel protocol – Yunhao Zheng et al. – Journal of Aerosol Science

Bacteria Facilitate Enteric Virus Co-infection of Mammalian Cells and Promote Genetic Recombination – Andrea K. Erickson et al. – Cell Host & Microbe

Human airway microbiome

Review: Airway microbial metagenomics – Katarzyna Pienkowska et al. – Microbes and Infection

Respiratory syncytial virus and rhinovirus bronchiolitis are associated with distinct metabolic pathways – Christopher J Stewart et al. – Journal of Infectious Diseases

Tech Note: A breath of information: the volatilome – M. Mansurova et al. – Current Genetics

Short-term particulate matter exposure influences nasal microbiota in a population of healthy subjects – Jacopo Mariani et al. – Environmental Research

Exposure to traffic-related air pollution and the composition of the gut microbiota in overweight and obese adolescents – Tanya L. Alderete et al. – Environmental Research

Human gut microbiome

Gut microbiome contributes to impairment of immunity in pulmonary tuberculosis patients by alteration of butyrate and propionate producers – Abhijit Maji et al. – Environmental Microbiology

Review: Targeting the gut barrier for the treatment of alcoholic liver disease – Zhanxiang Zhou and Wei Zhong – Liver Research

Review: Microbial Regulation of Glucose Metabolism and Insulin Resistance – Crommen S and Simon MC – Genes

Review: Gut microbiota in the pathogenesis of inflammatory bowel disease – Nishida A et al. – Clinical Journal of Gastroenterology

Review: Human Intestinal Microbiota: Interaction Between Parasites and the Host Immune Response – Oswaldo Partida-Rodríguez et al. – Archives of Medical Research

Review: Gut dysbiosis and irritable bowel syndrome: the potential role of probiotics – Nicola Principi et al. – Journal of Infection

Review: Gut Microbiota in Obesity and Metabolic Abnormalities: A Matter of Composition or Functionality? – Sofia Moran-Ramo et al. – Archives of Medical Research

In vitro: An in vitro study to assess the impact of tetracycline on the human intestinal microbiome – Ji Young Jung et al. – Anaerobe

Human gut-microbiome-brain axis

Review: Targeting gut microbiome: A novel and potential therapy for autism – Yongshou Yang et al. – Life Sciences

Metabolomics

Dark matter in host-microbiome metabolomics: Tackling the unknowns–A review – B.Y. Loulou Peisl et al. – Analytica Chimica Acta

Animal experiments

Mouse: Intestinal Ralstonia pickettii augments glucose intolerance in obesity – Shanthadevi D. Udayappan et al. – PLoS One

Pig: Structural Modulation of Gut Microbiota during Alleviation of Suckling Piglets Diarrhoea with Herbal Formula – Cui Liu et al. – Evidence-Based Complementary and Alternative Medicine

Rat: Effects of HLA-B27 on Gut Microbiota in Experimental Spondyloarthritis Implicate an Ecological Model of Dysbiosis – Gill T et al. – Arthritis and Rheumatology

Changes in mouse gut bacterial community in response to different types of drinking water – Marcela F. Dias et al. – Water Research

Mouse: Particle size determines the anti-inflammatory effect of wheat bran in a model of fructose over-consumption: Implication of the gut microbiota – Francesco Suriano & Audrey M. Neyrinck et al. – Journal of Functional Foods

Mouse: Mushroom polysaccharides from Ganoderma lucidum and Poria cocos reveal prebiotic functions – Imran Khan et al. – Journal of Functional Foods

Animal microbiome

Bacterial diversity of wild-caught Lutzomyia longipalpis (a vector of zoonotic visceral leishmaniasis in Brazil) under distinct physiological conditions by metagenomics analysis – Ana Clara Araújo Machado Pires et al. – Parasites & Vectors

Drosophila Perpetuates Nutritional Mutualism by Promoting the Fitness of Its Intestinal Symbiont Lactobacillus plantarum – Gilles Storelli et al. – Cell Metabolism

Analysis of the influence of living environment and age on vaginal fungal microbiome in giant pandas (Ailuropoda melanoleuca) by high throughput sequencing – Danyu Chen et al. – Microbial Pathogenesis

Plant, root and soil microbiome

Phosphate levels influence the utilisation of rice rhizodeposition carbon and the phosphate-solubilising microbial community in a paddy soil – Xi-En Long et al. – Soil Biology and Biochemistry

Plant community and soil conditions individually affect soil microbial community assembly in experimental mesocosms – Aspen T. Reese et al. – Ecology and Evolution

Responses of bulk and rhizosphere soil microbial communities to thermoclimatic changes in a Mediterranean ecosystem – Javier Pascual et al. – Soil Biology and Biochemistry

Remediation of arsenic in mung bean (Vigna radiata) with growth enhancement by unique arsenic-resistant bacterium Acinetobacter lwoffii – Joyati Das and Priyabrata Sarkar – Science of the Total Environment
https://www.sciencedirect.com/science/article/pii/S0048969717335830

* Opinion: Why we need a National Living Soil Repository – Daniel K. Manter et al. – PNAS

Long-term effects of nitrogen fertilization on aggregation and localization of carbon, nitrogen and microbial activities in soil – Yidong Wang et al. – Science of the Total Environment

Vineyard microbiome variations during different fertilisation practices revealed by 16s rRNA gene sequencing – Loredana Canfora et al. – Applied Soil Ecology

* Co-occurrence patterns of soybean rhizosphere microbiome at a continental scale – Baogang Zhang et al. – Soil Biology and Biochemistry

Review: Symbiotic nitrogen fixation by rhizobia — the roots of a success story – Catherine Masson-Boivin and Joel L Sachs – Current Opinion in Plant Biology

Water and extremophile microbiome

PDF: From extreme environments to human pathogens: an evolutionary journey – Donato Giovannelli and Costantino Vetriani – Biochemical Society

Comparison of Iris pseudacorus wetland systems with unplanted systems on pollutant removal and microbial community under nanosilver exposure – Juan Huang et al. – Science of the Total Environment

Impacts of design configuration and plants on the functionality of the microbial community of mesocosm-scale constructed wetlands treating ibuprofen – Liang Zhang et al. – Water Research

Microbial community evolution in partial nitritation/anammox process: From sidestream to mainstream – Yandong Yang et al. – Bioresource Technology

Spatiotemporal changes in bacterial community and microbial activity in a full-scale drinking water treatment plant – Luanfeng Hou et al. – Science of the Total Environment

Built environment microbiome

Microbiological air contamination in university premises and the evaluation of drug resistance of staphylococci occurring in the form of a bioaerosol – Katarzyna Wolny-Koładka et al. – Indoor and Built Environment

Phages and viruses

Virome analysis of lily plants reveals a new potyvirus – Yongqiang Li et al. – Archives of Virology

Comparative Analysis of 37 Acinetobacter Bacteriophages – Dann Turner et al. – Viruses

Antiviral systems in vector mosquitoes – Tong Liu et al. – Developmental & Comparative Immunology

Microbes in the news

Launceston associate professors studying gut microbiome in elderly Tasmanians – Carly Dolan – Examiner

Biofilm made of mulberry silk to destroy dengue virus – TNN – Times of India

Rhode Island Health Department finds E. coli bacteria, issues boil water notice – PATRICIA RESENDE & TONY GUGLIOTT – NBC 10

Op-Ed: Survival tips in the age of drug-resistant bacteria – Kevin Kavanagh – Lexington Herald Leader

* One Big Family: This Beautiful Interactive Diagram Shows How Every Organism Is Related – Fiona McMillan – Forbes

Researchers propose different approach to beat antibiotic-resistant superbugs – News Medical

 

December 30, 2017

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Enjoy your daily dose of (mostly human gut) microbiome literature!

General microbiome

Q&A: Friends (but sometimes foes) within: the complex evolutionary ecology of symbioses between host and microbes – Nicole Gerardo, BMC Biology

The Dark Side of IFN-γ: Its Role in Promoting Cancer Immunoevasion – Marija Mojic, International Journal of Molecular Sciences

Two-stage pretreatment of excess sludge for electricity generation in microbial fuel cell – Yi Zhang, Environmental Technology

Human respiratory microbiome

Azithromycin versus placebo for the treatment of HIV-associated chronic lung disease in children and adolescents (BREATHE trial): study protocol for a randomised controlled trial – Carmen Gonzalez-Martinez, BMC Biology

Human skin microbiome

Characterization of the facial microbiome in twins discordant for rosacea – Asifa K. Zaidi, Experimental Dermatology

Human oral microbiome

Oral health in geroscience: animal models and the aging oral cavity – Jonathan Y. An, GeroScience

Extracellular matrix Influence in Streptococcus mutans gene expression in a cariogenic biofilm – Elkin Jahir Florez Salamanca, Molecular Oral Microbiology

Human gut microbiome

The Microbiome–Gut–Behavior Axis: Crosstalk Between the Gut Microbiome and Oligodendrocytes Modulates Behavioral Responses – Achilles Ntranos, Neurotherapeutics

Antibiotics Associated Disorders and Postbiotics Induced Rescue in Gut Health – Debarati Paul, Current Pharmaceutical Design

We are not alone in our body: insights into the involvement of microbiota in the etiopathogenesis and pharmacology of mental illness –  Claudia Pisanu, Current Drug Metabolism

Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003 – Francesca Bottacini, BMC Genomics

Microbiota dysbiosis in inflammatory bowel diseases: in silico investigation of the oxygen hypothesis – Michael A. Henson, BMC Systems Biology

Gut microbiota: Fibre restores healthy gut microbiota – Alan Morris, Nature Reviews Endocrinology

The human microbiome in evolution – Emily R. Davenport, BMC Biology

Clinical characteristics and long-term prognosis of elderly onset ulcerative colitis – Eun Mi Song, Gastroenterology and Hepatology

Environmental contributions to gastrointestinal and liver cancer in the Asia–Pacific region – Kwang-Pil Ko, Gastroenterology and Hepatology

Effect of oral tobacco use and smoking on outcomes of Crohn’s disease in India – Umang Arora, Gastroenterology and Hepatology

Irritable bowel syndrome in Asia: Pathogenesis, natural history, epidemiology, and management – Kok-Ann Gwee, Gastroenterology and Hepatology

Rifaximin has minor effects on bacterial composition, inflammation, and bacterial translocation in cirrhosis: A randomized trial – Nina Kimer, Gastroenterology and Hepatology

The role of the microbiome and the use of probiotics in gastrointestinal disorders in adults in the Asia-Pacific region – background and recommendations of a regional consensus meeting – Uday C Ghoshal, Gastroenterology and Hepatology

Animal experiments

Inclusion of Bacillus amyloliquefaciensstrain TOA5001 in the diet of broilers suppresses the symptoms of coccidiosis by modulating intestinal microbiota – Takamitsu Tsukahara, Animal Science Journal

Characterization of the cervical bacterial community in dairy cows with metritis and during different physiological phases – Yu Wang, Theriogenology

Replacement of alfalfa hay (Medicago sativa L.) with subabul (Leucaena leucocephala) leaf meal in diets of Najdi goats: effect on digestion activity of rumen microorganisms – Tahereh Mohammadabadi, Tropical Animal Health and Production

Animal microbiome

Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing – Kathrin Engel, Microbial Ecology

Plant, root, and soil microbiome

Changes of microbial population and N-cycling function genes with depth in three Chinese paddy soils – Huanhuan Wang, PLOS One

Water and extremophile microbiome

Candidatus Nitrosocaldus cavascurensis, an ammonia oxidizing, extremely thermophilic archaeon with a highly mobile genome – Sophie S Abby, bioRxiv

Microbes in the news

Artificial intelligence identifies bacteria images quickly, accurately – Greg Slabodkin, Health Data Management

Microbes on the market

Assembly Biosciences, Inc. (ASMB) Reaches $45.08 After 7.00% Up Move; GEOX SPA (GXSBF) Shorts Raised By 18.36% – Stephen Andrade, Herald KS

December 29, 2017

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It’s a bit quiet towards the end of the year, but not without highlights. Could we fight antibiotic resistance by targeting mild infections using alternative drugs? Do we want to correct our own genes using CRISPR and what’s the future for penicillin?

Jobs

Associate Professor – Microbiology – Dental College -chennai

General microbiology

Efficient Hydrogen-Dependent Carbon Dioxide Reduction by Escherichia coli – Magali Roger et al. – Current Biology

Press: Bacteria under pressure run reaction in reverse to sequester carbon – John Timmer – Ars Technica

The Role of Type VI Secretion System Effectors in Target Cell Lysis and Subsequent Horizontal Gene Transfer – Peter David Ringel et al. – Cell Reports

Press: Predatory Bacteria Acquire Drug Resistance Directly from Rivals – Genetic Engineering & Biotechnology News

* Alternative therapeutics for self-limiting infections—An indirect approach to the antibiotic resistance challenge – Kristofer Wollein Waldetoft and Sam P. Brown – PLoS Biology

Author interview: Alternatives to Antibiotics: Why managing mild maladies matters – Beth Baker – PLoS Research News

Animal experiments

Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets – María Carla Piazzon et al. – Microbiome

Animal microbiome

Mosquito vector-associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod-borne diseases – Panpim Thongsripong et al. – Ecology and Evolution

Plant, root and soil microbiome

Rhizosphere-associated Alcaligenes and Bacillus strains that induce resistance against blast and sheath blight diseases, enhance plant growth and improve mineral content in rice – Kaleem U. Kakar et al. – Journal of Applied Microbiology

Microbes in the news

A week of holiday junk food could derail your gut microbiome—but there’s hope – Claire Maldarelli – Popular Science

Microbiota and Cancer – Andrea S. Blevins Prime – Cancer Therapy Advisor

Maternal Antibiotic Exposure Affects Infant Fecal Microbiota Following Vaginal Delivery – Jessica Martin – Infectious Disease Advisor

Microbe expert claims we should wash them ‘AT LEAST’ once a week at a high temperature to avoid dust mites and bacteria – Unity Blott – Daily Mail

* CORRECTING THE GENES – Santanu Chakraborty – Bangalore Mirror

Govt study finds faecal bacteria in 97 percent ‘filtered’ water jars in Dhaka – Bdnews24

* 200 million lives saved – but prognosis for penicillin is not healthy – Harry Ridgewell and Angela Long (collaborator) – Wiki Tribune

Microbes on the market

Report on sale: Human Microbiome Therapeutics Market is expected to Witness a CAGR of 14.19 % Till 2022 including Key Players: Rebiotix, Seres Therapeutics – Craig Francis – Social Articles Tracking & PR news.com

Report on sale: Microbiome Drugs Market by Production, Capacity Utilization Rate, Ex-Factory Price, Revenue, Cost, Gross and Gross Margin Analysis – Amit Pawar – Social Articles Tracking & PR news.com

 

December 22, 2017

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As the end of this year approaches, we have a post filled with plant/soil microbiome papers, as well as a few interesting food microbiology papers — enjoy!

General microbiome

A population genomics approach shows widespread geographical distribution of cryptic genomic forms of the symbiotic fungus Rhizophagus irregularis – Romain Savary, ISME

Pregnancy and early life

Gut microbiome in gestational diabetes: a cross-sectional study of mothers and offspring 5 years postpartum – Sayyid Hasan, Acta Obstetricia et Gynecologica Scandinavica

Liver microbiome

Environmental peer pressure: CD4+ T cell help in tolerance and transplantation – Dana Tedesco, Liver Transplantation

Skin microbiome

Food allergy and atopic dermatitis: Prediction, progression, and prevention – Carla Mastrorilli, Pediatric Allergy and Immunology

Respiratory microbiome

The Lung Microbiome in Idiopathic Pulmonary Fibrosis: A Promising Approach for Targeted Therapies – Fastrès Aline, International Journal of Molecular Sciences

Allergy – European Journal of Allergy and Clinical Immunology

Plant, root, and soil microbiome

Microbial and organic matter patterns in a prescribed burned and thinned managed forest ecosystem – Dessy A. Owiti, Ecosphere

Microbial Interactions and Perspectives for Bioremediation of Pesticides in the Soils – Ratna Prabha, Plant-Microbe Interactions in Agro-Ecological Perspectives

Fungi: An Effective Tool for Bioremediation – Sachin Gupta, Plant-Microbe Interactions in Agro-Ecological Perspectives

Arbuscular Mycorrhizal Fungi Improve Tolerance of Agricultural Plants to Cope Abiotic Stress Conditions – Pablo Cornejo, Plant-Microbe Interactions in Agro-Ecological Perspectives

Assessment of bacterial communities of black soybean grown in fields – Akifumi Sugiyama, Communicative & Integrative Biology

Plant-plant competition outcomes are modulated by plant effects on the soil bacterial community – S. Hortal, Scientific Reports

Trichoderma and Its Potential Applications – Monika Jangir, Plant-Microbe Interactions in Agro-Ecological Perspectives

Bacterial Rhizoremediation of Petroleum Hydrocarbons (PHC) – Jai Godheja, Plant-Microbe Interactions in Agro-Ecological Perspectives

Potential of Beneficial Bacteria as Eco-friendly Options for Chemical-Free Alternative Agriculture – Ch. Srinivasarao, Plant-Microbe Interactions in Agro-Ecological Perspectives

Potential Microbiological Approaches for the Remediation of Heavy Metal-Contaminated Soils – R. Krishnamoorthy, Plant-Microbe Interactions in Agro-Ecological Perspectives

Commercial Microbial Products: Exploiting Beneficial Plant-Microbe Interaction – Pallavi, Plant-Microbe Interactions in Agro-Ecological Perspectives

Interaction Between Beneficial Bacteria and Sugarcane – Guilherme Grodzki Oliveira Figueiredo, Plant-Microbe Interactions in Agro-Ecological Perspectives

Potential for Developing Low-Input Sustainable Agriculture in the Tropical Andes by Making Use of Native Microbial Resources – Luis Andrés Yarzábal, Plant-Microbe Interactions in Agro-Ecological Perspectives

Plant-Microbe Interactions in the Rhizosphere: Mechanisms and Their Ecological Benefits – Kulandaivelu Velmourougane, Plant-Microbe Interactions in Agro-Ecological Perspectives

Plant Interaction with Methylotrophic Communities – Manish Kumar, Plant-Microbe Interactions in Agro-Ecological Perspectives

Toward an Integrated Resource Management: Harnessing Trichoderma for Sustainable Intensification in Agriculture – Sumita Pal, Plant-Microbe Interactions in Agro-Ecological Perspectives,

Harnessing the Plant Microbiome: A Key Towards Sustainable Agriculture – Sanjana Kaul, Plant-Microbe Interactions in Agro-Ecological Perspectives

Rhizoremediation of Environmental Contaminants Using Microbial Communities – Ashish A. Prabhu, Plant-Microbe Interactions in Agro-Ecological Perspectives

Role of Plant Growth-Promoting Rhizobacteria for Improving Crop Productivity in Sustainable Agriculture – Abhijeet S. Kashyap, Plant-Microbe Interactions in Agro-Ecological Perspectives

Molecular evidence strongly supports deadwood-inhabiting fungi exhibiting unexpected tree species preferences in temperate forests – Witoon Purahong, ISME

Animal microbiome

Rare symbionts may contribute to the resilience of coral–algal assemblages – Maren Ziegler, ISME

Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton – Anny Cárdenas, ISME

Evidence for a primate origin of zoonotic Helicobacter suis colonizing domesticated pigs – Bram Flahou, ISME

Water and extremophile microbiome

Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates – Jürgen F H Strassert, ISME

Aquatic urban ecology at the scale of a capital: community structure and interactions in street gutters – Vincent Hervé, ISME

Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment – Kohei Ino, ISME

Food microbiome

Evaluation of the use of malic acid decarboxylase-deficient starter culture in NaCl-free cucumber fermentations to reduce bloater incidence – Y. Zhai, Journal of Applied Microbiology

Effect of phenolic compounds on the growth of selected probiotic and pathogenic bacteria – R. Pacheco-Ordaz, Letters in Applied Microbiology

Recent advances in the microencapsulation of omega-3 oil and probiotic bacteria through complex coacervation: A review – Divya Eratte, Trends in Food Science & Technology

Q fever and prevalence of Coxiella burnetii in milk – Andreana Pexara, Trends in Food Science & Technology

Microbes and art

Bioessays Cover Art